You can also say, "It rose by 3%" if you're talking about past tense, this is a simple/natural way to say it. Great question :)

Greetings Shia, - 'there is a rise of 3 % in ...... ' this expression is right. Because rise is verb.If you want to use 'by', then it will become passive voice and you have use ' the rate is risen by 3%'. Hope it would help! Happy Learning Deepika Mantra